[Biojava-l] BioJava 3Proposal tasks

[jitesh dundas]

Dear All,

Sorry I am sending this again ,but I don't see it in the list
anywhere.please post it.

I went through the BioJava3 proposal as you mentioned earlier..There
are a few things that I could take up without much worries...

 I can find out how Hibernate can be best deployed for BioJava. PLease
note that I suggest we use only hibernate3 or higher versions.
HIbernate2 has implementation and performace issues..
 I can also look at Spring after this task is done..

 I can find out the architectural and implementation issues in
Biojava. I am strong in Analysis and could do all this reasonably
well..

 I just want someone to share my concerns with and validate the findings..

 Analyse how BioJava is being used by the community. See the UsageAnalysis page.
 I can do these..
 To start from scratch, creating a number of smaller jars as
sub-projects within an umbrella BioJava3 project. Each jar would
provide tools for a specific purpose. Additional jars would provide
cross-purpose tools such as format converters or text-to-object
interfaces. Possibly built using Maven instead of Ant.
 Although starting from scratch, much existing code could be reused or
refactored to suit the new design.
 We would take full advantage of Java 6, including generics,
(@)annotations, the built-in property change support. Everything would
be a bean - absolutely everything.
 We would aim to be fully Java EE compliant, with the majority of
components fully reusable as a bean in any other application, just
like Spring's components are.
 We would adhere rigidly to a common coding style and heavily comment the code.
 We should make it able to focus on any aspect the user requires and
keep its efficiency, removing its dependency on everything being
sequence-related.
 SymbolLists and Alphabets to be rethought as these are the most
common stumbling block.
 Make methods parallel-aware and take advantage of this when possible,
and provide a global variable to specify how much parallelisation can
take place. - I am very interested in this and would liek to take this
up asap Sir.. JDK 1.5 has parallel programming extension to use and we
can define a common method or mode for executing existing code or
functionalities..However, impact analysis will be needed as NOT ALL
CODE CAN BE MADE PARALLEL COMPLIANT DUE TO IMPLEMENTATION ISSUES>>WILL
NEED THOROUGH CHECKING...i can do this..
 Please reply and advise which i should take up first ..Points in bold
are of particular interest to me..Even those beyond those list are
welcome ...

 Regards,
 JD